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Mol Cell. 2019 Nov 21;76(4):574-589.e7. doi: 10.1016/j.molcel.2019.08.013. Epub 2019 Sep 17.

Spatiotemporal Organization of the E. coli Transcriptome: Translation Independence and Engagement in Regulation.

Author information

1
Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel.
2
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02140, USA.
3
Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel. Electronic address: amster@cc.huji.ac.il.

Abstract

RNA localization in eukaryotes is a mechanism to regulate transcripts fate. Conversely, bacterial transcripts were not assumed to be specifically localized. We previously demonstrated that E. coli mRNAs may localize to where their products localize in a translation-independent manner, thus challenging the transcription-translation coupling extent. However, the scope of RNA localization in bacteria remained unknown. Here, we report the distribution of the E. coli transcriptome between the membrane, cytoplasm, and poles by combining cell fractionation with deep-sequencing (Rloc-seq). Our results reveal asymmetric RNA distribution on a transcriptome-wide scale, significantly correlating with proteome localization and prevalence of translation-independent RNA localization. The poles are enriched with stress-related mRNAs and small RNAs, the latter becoming further enriched upon stress in an Hfq-dependent manner. Genome organization may play a role in localizing membrane protein-encoding transcripts. Our results show an unexpected level of intricacy in bacterial transcriptome organization and highlight the poles as hubs for regulation.

KEYWORDS:

E. coli; RNA localization; RNA sequencing; bacteria; cell fractionation; live-cell microscopy; small RNAs; spatial organization

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